Sequence Unique database used by WHAT IF

The PDB structures stored in the WHAT IF relational database are a representative set of sequence-unique structures generated from the X-ray protein PDB files available at a certain moment.

The procedure used to generate this database is similar to the PDB select algorithm, but rather than focusing on maximum size of the subset, our algorithm focuses on getting representative structures of the highest available quality. For the selection an empirical quality value is defined: a composite score depending on the Resolution and the R-factor (published funny enough in: Verification of protein structures: Side-chain planarity. R.W.W. Hooft, C.Sander and G.Vriend, J. Appl. Cryst. (1996) 29, 714-716. ). However, we use a sequence identy percentage cutoff of 30%, respectively 90%, and the resolution and R-factor criteria are as indicated below.

Each structure is identified by the 4-letter PDB identifier, plus (if applicable) a one-letter chain name. Structures are ordered by decreasing 'quality value' as described in the article cited above.

The data

R-factor<0.25 and Resolution<2.5

• List of 774 PDB chains, created from the PDB on August 13 1998
• List of 840 PDB chains, created from the PDB on January 08 1999
• List of 888 PDB chains, created from the PDB on March 03 1999
• List of 967 PDB chains, created from the PDB on June 22 1999

R-factor<0.21 and Resolution<2.1

• List of 283 PDB chains, created from the PDB on May 6 1996
• List of 295 PDB chains, created from the PDB on June 25 1996
• List of 304 PDB chains, created from the PDB on July 25 1996
• List of 308 PDB chains, created from the PDB on August 20 1996
• List of 315 PDB chains, created from the PDB on September 23 1996
• List of 319 PDB chains, created from the PDB on October 18 1996
• List of 478 PDB chains, created from the PDB on April 17 1998
• List of 548 PDB chains, created from the PDB on January 6 1999
• List of 634 PDB chains, created from the PDB on June22 1999

R-factor<0.21 and Resolution<2.0

• List of 253 PDB chains, created from the PDB on November 12 1996
• List of 259 PDB chains, created from the PDB on December 11 1996
• List of 274 PDB chains, created from the PDB on February 10 1997
• List of 279 PDB chains, created from the PDB on February 18 1997
• List of 296 PDB chains, created from the PDB on April 10 1997
• List of 303 PDB chains, created from the PDB on April 25 1997
• List of 309 PDB chains, created from the PDB on May 27 1997
• List of 312 PDB chains, created from the PDB on July 23 1997
• List of 368 PDB chains, created from the PDB on April 17 1998
• List of 387 PDB chains, created from the PDB on August 02 1998
• List of 432 PDB chains, created from the PDB on January 05 1999
• List of 462 PDB chains, created from the PDB on March 06 1999
• List of 511 PDB chains, created from the PDB on June 22 1999

R-factor<0.20 and Resolution<1.9

• List of 282 PDB chains, created from the PDB on April 17 1998
• List of 296 PDB chains, created from the PDB on August 02 1998
• List of 318 PDB chains, created from the PDB on January 05 1999
• List of 344 PDB chains, created from the PDB on March 07 1999
• List of 372 PDB chains, created from the PDB on June 22 1999

R-factor<0.18 and Resolution<1.8

• List of 135 PDB chains, created from the PDB on April 17 1998
• List of 139 PDB chains, created from the PDB on August 10 1998
• List of 144 PDB chains, created from the PDB on January 04 1999
• List of 154 PDB chains, created from the PDB on March 07 1999
• List of 172 PDB chains, created from the PDB on June 22 1999

R-factor<0.19 and Resolution<1.7

• List of 117 PDB chains, created from the PDB on April 17 1998
• List of 134 PDB chains, created from the PDB on January 3 1999
• List of 142 PDB chains, created from the PDB on March 07 1999
• List of 156 PDB chains, created from the PDB on June 22 1999

R-factor<0.19 and Resolution<1.6

• List of 65 PDB chains, created from the PDB on April 17 1998
• List of 78 PDB chains, created from the PDB on January 3 1999
• List of 81 PDB chains, created from the PDB on March 07 1999
• List of 91 PDB chains, created from the PDB on June 22 1999

R-factor<0.19 and Resolution<1.5

• List of 39 PDB chains, created from the PDB on April 17 1998
• List of 47 PDB chains, created from the PDB on January 3 1999
• List of 48 PDB chains, created from the PDB on March 07 1999
• List of 48 PDB chains, created from the PDB on June 22 1999

Tables for 90% identity cutoff

R-factor<0.25 and Resolution<2.5 at <90% sequence identity

• List of 1619 PDB chains, created from the PDB on June 22 1999

R-factor<0.21 and Resolution<2.1 at <90% sequence identity

• List of 982 PDB chains, created from the PDB on June 22 1999

R-factor<0.21 and Resolution<2.0 at <90% sequence identity

• List of 769 PDB chains, created from the PDB on June 22 1999

R-factor<0.20 and Resolution<1.9 at <90% sequence identity

• List of 539 PDB chains, created from the PDB on June 22 1999

R-factor<0.18 and Resolution<1.8 at <90% sequence identity

• List of 228 PDB chains, created from the PDB on June 22 1999

R-factor<0.19 and Resolution<1.7 at <90% sequence identity

• List of 203 PDB chains, created from the PDB on June 22 1999

R-factor<0.19 and Resolution<1.5 at <90% sequence identity

• List of 66 PDB chains, created from the PDB on June 22 1999

Last modified June 22 1999